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Histone demethylation mediated by the nuclear amine oxidase homolog LSD1

a nuclear amine oxidase and histone demethylation technology, applied in the field of gene regulation, can solve the problems of unclear whether bona fide histone demethylases exist, the molecular identity of these putative histone demethylases remains elusive, and cannot allow dynamic regulation of histone methylation

Active Publication Date: 2010-06-22
PRESIDENT & FELLOWS OF HARVARD COLLEGE
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  • Summary
  • Abstract
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  • Claims
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AI Technical Summary

Benefits of technology

The patent text describes methods for monitoring and regulating the activity of eukaryotic histone demethylase proteins. These methods involve contacting a histone demethylase protein with a histone peptide that is methylated or unmethylated, and determining the methylation status of the histone peptide. The methods can be used to screen for modulators of histone demethylase activity and to up- or down-regulate the expression of genes that are activated or repressed by methylation. The patent also describes methods for identifying agents that modulate the interaction between a histone demethylase protein and a CoREST protein. Overall, the patent provides tools for studying the function and regulation of histone demethylase proteins.

Problems solved by technology

However, this mechanism would not allow for dynamic regulation of histone methylation and the plasticity that may be essential for gene transcription regulation in some biological processes.
However, since PAD14 / PAD4 catalyzes deimination but not demethylation, it remains unclear whether bona fide histone demethylases exist.
These early studies suggested the possibility that histone demethylases may exist but the molecular identity of these putative histone demethylases have remained elusive for the past four decades.

Method used

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  • Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
  • Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
  • Histone demethylation mediated by the nuclear amine oxidase homolog LSD1

Examples

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example 1

[0115]To understand the function and mechanism of action of KIAA0601, we undertook molecular, biochemical and enzymological analyses of the protein. Using multiple experimental approaches, we demonstrate that KIAA0601 is a lysine-specific demethylase with substrate specificity for K4 methylated histone H3. We now refer to protein as LSD1 (Lysine Specific Demethylase 1) to reflect this newly identified role. The text and figures corresponding to this example may be found in Shi et al. Cell (2004) 119:903, which is specifically incorporated by reference herein.

[0116]LSD1 is a Transcriptional Co-repressor that is Evolutionarily Conserved

[0117]FIG. 1A shows a schematic diagram of the predicted domains of LSD1 and its related proteins. The C-terminal 2 / 3 of LSD1 display significant sequence homology with FAD-dependent amine oxidases. The N-terminus of LSD1 has a SWIRM domain, which is found in a number of proteins involved in chromatin regulation (Aravind and Iyer, 2002). Although the fu...

example 2

[0119]LSD1 is a Lysine-specific Histone Demethylase

[0120]LSD1 is a flavin-containing protein based on its ability to bind FAD ((Humphrey et al., 2001), and data not shown). Its sequence homology with amine oxidases predicts that LSD1 may catalyze oxidation reactions of biogenic amines including monoamine, polyamines or N-methylated protein substrates (such as histones) (Bannister et al., 2002). Amine oxidation catalyzed by flavin-containing amine oxidase is characterized by oxidative cleavage of the α-carbon bond of the substrate to form an imine intermediate, which, in turn, is hydrolyzed to form an aldehyde and amine via a non-enzymatic process. In a complete catalytic cycle, the cofactor FAD is reduced to FADH2 and then is likely to be re-oxidized by oxygen to produce hydrogen peroxide (Binda et al., 2002). We hypothesized that, as a flavin-containing amine oxidase homolog, LSD1 may catalyze the conversion of mono- or dimethylated K (or R) to non-methylated K (or R) and formaldeh...

example 3

[0124]LSD1-mediated Histone Demethylation Generates Formaldehyde

[0125]We used a third independent method to investigate the possibility that LSD1 is a histone demethylase. As shown in FIG. 2, the demethylation reaction mediated by LSD1 is predicted to generate formaldehyde. To determine whether formaldehyde was produced in LSD1-mediated enzymatic reactions, we first used the formaldehyde dehydrogenase (FDH) assay to detect the presence of formaldehyde (Lizcano et al., 2000). This assay employs formaldehyde dehydrogenase to convert formaldehyde to formic acid using NAD+ as the electron acceptor, whose reduction to NADH can be spectrophotometrically measured at OD 340 nm. Thus, when the demethylation reaction is coupled with the FDH assay, the enzymatic activity of LSD1 and reaction kinetics can be determined by measuring the production of NADH. A standard curve was first generated using purified FDH (EC 1.2.1.46), NAD+ and different concentrations of formaldehyde ranging from 1 μM to...

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Abstract

LSD1, a homolog of nuclear amine oxidases, functions as a histone demethylase and transcriptional co-repressor. LSD1 specifically demethylates histone H3 lysine 4, which is linked to active transcription. Lysine demethylation occurs via an oxidation reaction that generates formaldehyde. Importantly, RNAi inhibition of LSD1 causes an increase in H3 lysine 4 methylation and concomitant de-repression of target genes, suggesting that LSD1 represses transcription via histone demethylation. The results thus identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histone methylases and demethylases.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application is the National Stage of International Application No. PCT / US2005 / 045987, filed Dec. 16, 2005, which claims the benefit of Provisional Application No. 60 / 636,095, filed Dec. 16, 2004, both of which are specifically incorporated by reference herein.GOVERNMENT INTEREST[0002]This invention was made using funds from grant GM071004 from the U.S. National Institutes of Health. The U.S. government therefore retains certain rights in the invention.TECHNICAL FIELD OF THE INVENTION[0003]This invention is related to the area of gene regulation. In particular, it relates to the area of modification of chromosome structure as a means of regulating transcription. This modification importantly impacts disease processes as well as normal physiology and development.BACKGROUND OF THE INVENTION[0004]The histone N-terminal tails are subjected to multiple covalent modifications that affect chromatin structure and consequently transcription. O...

Claims

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Application Information

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Patent Type & Authority Patents(United States)
IPC IPC(8): C12N9/00C12N15/09
CPCC12Q1/26A61K45/06A61K31/713G01N2333/906G01N2500/02A61P35/00A61P43/00
Inventor SHI, YANGSHI, YUJIANG
Owner PRESIDENT & FELLOWS OF HARVARD COLLEGE
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